![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 hours ago
#19734 new defect
ChimeraX bug report submission
| Reported by: | Zach Pearson | Owned by: | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.12.dev202601082324 (2026-01-08 23:24:27 UTC)
Description
two stars missing in xyloglucan.pdb
Log:
UCSF ChimeraX version: 1.12.dev202601082324 (2026-01-08)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zjp/Downloads/emd_39496.map format ccp4
Opened emd_39496.map as #1, grid size 256,256,256, pixel 1.09, shown at level
0.188, step 1, values float32
> ui tool show lightin
> lighting intensity 1.34
> lighting fillIntensity 0.72
> lighting ambientColor 251,255,249
> lighting ambientColor 254,255,251
> lighting ambientColor 255,248,251
> lighting ambientColor 255,236,250
> lighting ambientColor 255,223,248
> lighting ambientColor 255,198,245
> lighting ambientColor 255,190,243
> lighting ambientColor 255,184,242
> lighting ambientColor 255,180,242
> lighting ambientColor 255,178,241
> lighting ambientColor 255,176,241
> lighting ambientColor 255,174,242
> lighting ambientColor 255,172,243
> lighting ambientColor 255,170,244
> lighting ambientColor 255,166,246
> lighting ambientColor 255,162,247
> lighting ambientColor 255,157,248
> lighting ambientColor 255,152,250
> lighting ambientColor 255,147,251
> lighting ambientColor 255,140,254
> lighting ambientColor 253,133,255
> lighting ambientColor 249,124,255
> lighting ambientColor 245,116,255
> lighting ambientColor 241,109,255
> lighting ambientColor 237,102,255
> lighting ambientColor 233,96,255
> lighting ambientColor 228,88,255
> lighting ambientColor 220,80,255
> lighting ambientColor 213,73,255
> lighting ambientColor 205,66,255
> lighting ambientColor 199,60,255
> lighting ambientColor 195,56,255
> lighting ambientColor 191,52,255
> lighting ambientColor 188,49,255
> lighting ambientColor 184,45,255
> lighting ambientColor 180,43,255
> lighting ambientColor 172,39,255
> lighting ambientColor 167,38,255
> lighting ambientColor 163,37,255
> lighting ambientColor 160,36,255
> lighting ambientColor 152,36,255
> lighting ambientColor 145,37,255
> lighting ambientColor 138,37,255
> lighting ambientColor 129,37,255
> lighting ambientColor 121,39,255
> lighting ambientColor 113,41,255
> lighting ambientColor 107,42,255
> lighting ambientColor 103,42,255
> lighting ambientColor 99,43,255
> lighting ambientColor 93,43,255
> lighting ambientColor 90,43,255
> lighting ambientColor 87,42,255
> lighting ambientColor 84,41,255
> lighting ambientColor 82,41,255
> lighting ambientColor 81,41,255
> lighting ambientColor 79,40,255
> lighting ambientColor 76,40,255
> lighting ambientColor 70,39,255
> lighting ambientColor 53,33,255
> lighting ambientColor 43,30,255
> lighting ambientColor 35,28,255
> lighting ambientColor 29,25,255
> lighting ambientColor 24,23,255
> lighting ambientColor 22,24,255
> lighting ambientColor 21,24,255
> lighting ambientColor 20,25,255
> lighting ambientColor 19,25,255
> lighting ambientColor 19,26,255
> lighting ambientColor 18,26,255
> lighting ambientColor 17,26,255
> lighting ambientColor 16,26,255
> lighting ambientColor 15,26,255
> lighting ambientColor 15,27,255
> lighting ambientColor 14,27,255
> lighting ambientColor 14,28,255
> lighting ambientColor 14,29,255
> lighting ambientColor 13,29,255
> lighting ambientColor 14,30,255
> lighting color 255,252,254
> lighting color 255,253,254
> lighting color 255,254,253
> lighting color 253,255,251
> lighting color 249,255,247
> lighting color 244,255,242
> lighting color 238,255,236
> lighting color 232,255,230
> lighting color 226,255,224
> lighting color 222,255,219
> lighting color 218,255,215
> lighting color 215,255,212
> lighting color 213,255,209
> lighting color 210,255,205
> lighting color 208,255,201
> lighting color 206,255,198
> lighting color 193,255,181
> lighting color 188,255,176
> lighting color 183,255,169
> lighting color 171,255,156
> lighting color 166,255,150
> lighting color 161,255,144
> lighting color 157,255,140
> lighting color 153,255,136
> lighting color 150,255,132
> lighting color 147,255,128
> lighting color 143,255,124
> lighting color 138,255,119
> lighting color 133,255,114
> lighting color 127,255,110
> lighting color 120,255,104
> lighting color 113,255,99
> lighting color 108,255,95
> lighting color 102,255,91
> lighting color 96,255,87
> lighting color 91,255,84
> lighting color 86,255,81
> lighting color 82,255,78
> lighting color 77,255,75
> lighting color 73,255,73
> lighting color 70,255,71
> lighting color 68,255,71
> lighting color 66,255,70
> lighting color 64,255,69
> lighting color 62,255,69
> lighting color 62,255,68
> lighting color 61,255,68
> lighting color 61,255,67
> lighting color 60,255,67
> lighting color 59,255,66
> lighting color 58,255,65
> lighting color 57,255,63
> lighting color 55,255,61
> lighting color 53,255,59
> lighting color 51,255,57
> lighting color 49,255,54
> lighting color 47,255,51
> lighting color 45,255,47
> lighting color 42,255,43
> lighting color 40,255,39
> lighting color 39,255,37
> lighting color 38,255,35
> lighting color 37,255,33
> lighting color 36,255,31
> lighting color 36,255,30
> lighting color 35,255,29
> lighting color 31,255,25
> lighting color 29,255,22
> lighting color 27,255,20
> lighting color 25,255,17
> lighting color 24,255,14
> lighting color 22,255,12
> lighting color 21,255,10
> lighting color 20,255,8
> lighting color 19,255,5
> lighting color 20,255,4
> lighting color 21,255,3
> lighting color 23,255,2
> lighting color 24,255,2
> lighting color 25,255,2
> lighting color 26,255,3
> lighting color 27,255,3
> lighting color 29,255,4
> lighting color 31,255,4
> lighting color 33,255,5
> lighting color 35,255,5
> lighting color 39,255,5
> lighting color 43,255,5
> lighting color 50,255,4
> lighting color 57,255,3
> lighting color 64,255,2
> lighting color 71,255,0
> lighting color 83,255,0
> lighting color 90,255,0
> lighting color 99,255,0
> lighting color 109,255,0
> lighting color 113,255,0
> lighting color 116,255,0
> lighting color 118,255,0
> lighting color 120,255,0
> lighting color 123,255,0
> lighting color 130,255,5
> lighting color 130,255,0
> lighting color 132,255,0
> lighting color 135,255,0
> lighting color 137,255,0
> lighting color 139,255,0
> lighting color 137,255,0
> material specularExponent 5.0
Expected one of 'chimera', 'default', 'dull', or 'shiny' or a keyword
> material reflectivity 0.38
> material specularExponent 13.0
Expected one of 'chimera', 'default', 'dull', or 'shiny' or a keyword
> ui tool show lightin
> close
> open /Users/zjp/Downloads/xyloglucan.pdb format pdb
> snfg show
Showing SNFG symbols for 8 carbohydrate residues
> select ~sel & ##selected
Nothing selected
> snfg show size 1
Showing SNFG symbols for 8 carbohydrate residues
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK193LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 15 days, 15 hours, 11 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
EPSON PJ:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AliasGUI: 1.0
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.62.0
ChimeraX-AtomicLibrary: 14.2.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202601082324
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8
ChimeraX-Label: 1.3
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.0
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.3
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.7
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.1
pyproject_hooks: 1.2.0
PyQt6: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.1
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.1.2
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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